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Fig. 4 | Clinical Epigenetics

Fig. 4

From: High-throughput and affordable genome-wide methylation profiling of circulating cell-free DNA by methylated DNA sequencing (MeD-seq) of LpnPI digested fragments

Fig. 4

The compatibility of vacuum concentrated samples in different buffers with MeD-seq analysis. The top two panels show results for 10 ng of genomic MCF7 DNA dissolved in AVE buffer, water, or Maxwell elution buffer analysed by MeD-seq with and without preceding vacuum concentration of the sample. In A the percentage of LpnpI filtered reads, and in B the percentage of duplicate reads is shown for the different elution buffers with (in black) and without (in grey) vacuum concentration. The middle two panels show results for different aliquots of 10 ng cfDNA from the same plasma sample dissolved in AVE buffer, water, or Maxwell elution buffer analysed by MeD-seq with and without preceding vacuum concentration of the sample. In C the percentage of LpnpI filtered reads, and in D the percentage of duplicate reads is shown for the different elution buffers with (in black) and without (in grey) vacuum concentration. E Principal components were calculated for cfDNA methylation profiles of genomic MCF7 DNA and 3 plasma aliquots from a single metastatic breast cancer patient dissolved in AVE (■), H2O (▲), MW () buffer with and without vacuum concentration. PC1 and PC2, with the explained variances, are shown on the x-axis and y-axis, respectively. Each icon represents 1 cfDNA sample: samples coloured in red and black were vacuum concentrated, whereas samples in orange and purple were not

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